From: Ashar Malik (
Date: Wed Dec 03 2014 - 01:13:42 CST

RMSD is a one to one comparison between two structures. Given structure A,
B, C and depending on how you are doing it, you could get one value for

A <> B
A <> C
B <> C

You haven't told us how you are calculating the RMSD. If you have a
trajectory, then by default the 0th frame becomes reference (this can be
changed) and you would have N-1 RMSD values where N is the total number of
structure that you have.

Again - more information is needed to correctly answer your question.

On Wed, Dec 3, 2014 at 7:53 PM, Seera Suryanarayana <>

> Dear VMD Users
> Is it possible to calculate the RMSD between three superimposed proteins?
> I have been tried in VMD by using three proteins and I got two values. It
> seems it has taken one protein as reference. Am I right?
> Surya
> Graduate student
> India.